Development of SSR markers using RNA-seq approach and genetic diversity of two populations of Asian moon scallop Amusium pleuronectes

Abstract

In this study, we obtained a batch of simple sequence repeats (SSRs) from the transcriptome data of Asian moon scallop Amusium pleuronectes and analyzed the distribution and frequency of these SSRs. A total of 7,315 SSRs were obtained from 159,521 unigenes. Bioinformatics tools were employed to design appropriate primers. A total of 4,038 SSR loci had flanking sequences suitable for polymerase chain reaction primer design. One hundred SSR primers were validated and the rate of successful amplification was 78.0%. Fourteen randomly chosen primer pairs were amplified in Beibu Bay population (BP) and Hainan Baimajing population (HP). The number of alleles at each locus ranged from 2 to 3 in two populations, with mean values of 2.214 and 2.143, respectively. The observed heterozygosity, expected heterozygosity and polymorphism information content of BP were 0.463, 0.646 and 0.281, respectively, while those of HP were 0.309, 0.320 and 0.259, respectively. The developed SSR markers will be helpful for further studies on population genetics, genetic linkage construction and chromosome linkage mapping in the species.